AFAIK is Atmel's Jtag protocol proprietary.
More of the newer data sheets contain everything you need to know to program over JTAG. Older data sheet didn't, although back in 2001 or thereabouts I worked at a place where we wanted to program AVRs in-circuit via JTAG, and at the time Atmel was willing to hand over the programming information if you signed an NDA with them.
Hence if anything I'd say Atmel is one of the easier parts to use if you want to program via JTAG.
That being said, the JTAG standard itself is a bit more complicated than SPI, so given the option, I'd chose the later.
---Joel